tbuckley/cabot-search huggingface dataset:
Ultrarare Coding Variants and Cognitive Function in Schizophrenia
Authors: Hugo D. J. Creeth, Elliott Rees, Sophie E. Legge, Charlotte A. Dennison, Peter Holmans, James T. R. Walters, Michael C. O’Donovan, Michael J. Owen
Journal: JAMA Psychiatry (2022)

Importance Impaired cognitive function in schizophrenia is associated with poor functional outcomes, but the role of rare coding variants is unclear. Objective To determine whether ultrarare constrained variants (URCVs) are associated with cognition in patients with schizophrenia. Design, Setting, and Participants Linear regression was used to perform a within-case genetic association study of URCVs and current cognition and premorbid cognitive ability. A multivariable linear regression analysis of the outcomes associated with URCVs, schizophrenia polygenic risk score, polygenic risk score for intelligence and schizophrenia associated copy number variants on cognitive ability was performed. Exome sequencing data from 802 participants with schizophrenia were assessed for current cognition using the Measurement and Treatment Research to Improve Cognition in Schizophrenia Consensus Cognitive Battery and for estimated premorbid IQ using the National Adult Reading Test. Individuals were recruited from clinical and voluntary mental health services in the UK. Those with a diagnosis of intellectual disability or a neurological disorder known to affect cognition were excluded. Data collection occurred between 2007 and 2015. Data were analyzed between April 2020 and March 2022. Main Outcomes and Measures Association between URCVs, current cognition, and current cognition adjusted for premorbid IQ. Results Of the 802 participants, 499 (62%) were men and 303 (38%) were women; mean (SD) age at interview was 43.36 (11.87) years. Ultrarare constrained variants (n = 400) were associated with lower current cognition scores (β = −0.18; SE = 0.07; P = .005). In the univariable analysis, premorbid IQ was associated with URCVs (β = −0.12; SE = 0.05; P = .02) and partly attenuated the association with current cognition (β = −0.09; SE = 0.05; P = .08). Multivariable analysis showed that measured genetic factors combined accounted for 6.2% of variance in current cognition, 10.3% of variance in premorbid IQ, and supported outcomes of URCVs associated with current cognition independent of premorbid IQ (β = −0.10; SE = 0.05; P = .03). Conclusions and Relevance The findings of this study suggest that URCVs contribute to variance in cognitive function in schizophrenia, with partly independent associations before and after onset of the disorder. Although the estimated effect sizes were small, future studies may show that the effect sizes will be greater with better annotation of pathogenic variants. Genomic data may contribute to identifying those at particularly high risk of cognitive impairment in whom early remedial or preventive measures can be implemented.
Association of Chronic Kidney Disease With Risk of Intracerebral Hemorrhage
Authors: Kevin N. Vanent, Audrey C. Leasure, Julian N. Acosta, Lindsey R. Kuohn, Daniel Woo, Santosh B. Murthy, Hooman Kamel, Steven R. Messé, Michael T. Mullen, Jordana B. Cohen, Debbie L. Cohen, Raymond R. Townsend, Nils H. Petersen, Lauren H. Sansing, Thomas M. Gill, Kevin N. Sheth, Guido J. Falcone
Journal: JAMA Neurology (2022)

The evidence linking chronic kidney disease (CKD) to spontaneous intracerebral hemorrhage (ICH) is inconclusive owing to possible confounding by comorbidities that frequently coexist in patients with these 2 diseases.To determine whether there is an association between CKD and ICH risk.A 3-stage study that combined observational and genetic analyses was conducted. First, the association between CKD and ICH risk was tested in the Ethnic/Racial Variations of Intracerebral Hemorrhage (ERICH) study, a multicenter case-control study in the US. All participants with available data on CKD from ERICH were included. Second, this analysis was replicated in the UK Biobank (UKB), an ongoing population study in the UK. All participants in the UKB were included in this study. Third, mendelian randomization analyses were implemented in the UKB using 27 CKD-related genetic variants to test for genetic associations. ERICH was conducted from August 1, 2010, to August 1, 2017, and observed participants for 1 year. The UKB enrolled participants between 2006 and 2010 and will continue to observe them for 30 years. Data analysis was performed from November 11, 2019, to May 10, 2022.CKD stages 1 to 5.The outcome of interest was ICH, ascertained in ERICH via expert review of neuroimages and in the UKB via a combination of self-reported data and International Statistical Classification of Diseases, Tenth Revision, codes.In the ERICH study, a total of 2914 participants with ICH and 2954 controls who had available data on CKD were evaluated (mean [SD] age, 61.6 [14.0] years; 2433 female participants [41.5%]; 3435 male participants [58.5%]); CKD was found to be independently associated with higher risk of ICH (odds ratio [OR], 1.95; 95% CI, 1.35-2.89; P < .001). This association was not modified by race and ethnicity. Replication in the UKB with 1341 participants with ICH and 501 195 controls (mean [SD] age, 56.5 [8.1] years; 273 402 female participants [54.4%]; 229 134 male participants [45.6%]) confirmed this association (OR, 1.28; 95% CI, 1.01-1.62; P = .04). Mendelian randomization analyses indicated that genetically determined CKD was associated with ICH risk (OR, 1.56; 95% CI, 1.13-2.16; P = .007).In this 3-stage study that combined observational and genetic analyses among study participants enrolled in 2 large observational studies with different characteristics and study designs, CKD was consistently associated with higher risk of ICH. Mendelian randomization analyses suggest that this association was causal. Further studies are needed to identify the specific biological pathways that mediate this association.
Activity of Cabazitaxel in Metastatic or Inoperable Locally Advanced Dedifferentiated Liposarcoma
Authors: Roberta Sanfilippo, Richard L. Hayward, Jammbe Musoro, Charlotte Benson, Michael Gordon Leahy, Antonella Brunello, Jean-Yves Blay, Neeltje Steeghs, Ingrid M. E. Desar, Nasim Ali, Alice Hervieu, Khin Thway, Sandrine Marreaud, Saskia Litiere, Bernd Kasper
Journal: JAMA Oncology (2022)

Treatment options for patients with unresectable and/or metastatic dedifferentiated liposarcoma (DDLPS) are limited. New drugs are required.To assess whether cabazitaxel demonstrated sufficient antitumor activity in patients with metastatic or inoperable locally advanced DDLPS to justify further investigation in a phase 3 setting.This international multicenter, open-label single-arm phase 2 trial was conducted at 10 institutions in 4 European countries from March 2015 to March 2019. Eligible patients had to have metastatic or locally advanced histologically proven DDLPS with evidence of disease progression within the past 6 months and had to have received no more than 1 previous line of chemotherapy.After mandatory central review of tumor blocks, if the DDLPS diagnosis was confirmed, patients started treatment within 72 hours after registration. Cabazitaxel was administered at a dose of 25 mg/m2 IV infusion over 1 hour every 21 days until intolerance, progression, or withdrawal of consent.The primary end point was progression-free survival (PFS) rate at 12 weeks per RECIST 1.1. Based on a Simon 2-stage design, at least 4 of 17 (stage 1) and 11 of 37 (stage 2) eligible and evaluable patients who were progression free at 12 weeks were needed. The final analysis report was completed on November 17, 2021.Forty patients were registered, with 2 patients being ineligible. The number of cycles ranged from 1 to 30, with a median of 5; 26 patients (65%) received at least 4 cycles of cabazitaxel. Progression-free survival at 12 weeks was 55%, achieving the primary study end point. At a median follow-up of 21.6 months, median PFS was 6 months and median OS 21 months. Response rate (RR) was 8% with 1 clinical response (CR) and 2 partial responses (PR). Twenty-three (60.5%) patients had a stable disease (SD). Disease control (PR+SD) was achieved in 26 patients (68%).This nonrandomized phase 2 clinical trial met its primary end point, with 21 of 38 patients (55%) being progression free at 12 weeks. These results suggest important activity of cabazitaxel in patients with metastatic or inoperable locally advanced DDLPS. The drug is worth being further studied in these tumors in a phase 3 setting.
Racial and Sex Disparities in Gout Prevalence Among US Adults
Authors: Natalie McCormick, Na Lu, Chio Yokose, Amit D. Joshi, Shanshan Sheehy, Lynn Rosenberg, Erica T. Warner, Nicola Dalbeth, Tony R. Merriman, Kenneth G. Saag, Yuqing Zhang, Hyon K. Choi
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Emerging data suggest gout and hyperuricemia may now be more frequent among Black adults in the US than White adults, especially Black women. However, national-level, sex-specific general population data on racial differences in gout prevalence and potential socioclinical risk factors are lacking. <h3>Objective</h3> To identify sex-specific factors driving disparities between Black and White adults in contemporary gout prevalence in the US general population. <h3>Design, Setting, and Participants</h3> This cross-sectional analysis used nationally representative, decadal survey data from successive cycles of the National Health and Nutrition Examination Survey from 2007 to 2016. Data were analyzed from November 1, 2019, through May 31, 2021. Participants included US adults self-reporting Black or White race. <h3>Exposures</h3> Self-reported race, excess body mass index, chronic kidney disease (CKD; defined as estimated glomerular filtration rate &lt;60 mL/min/1.73 m<sup>2</sup>, according to latest equations without race coefficient), poverty, poor-quality diet, low educational level, alcohol consumption, and diuretic use. <h3>Main Outcomes and Measures</h3> Race- and sex-specific prevalence of physician- or clinician-diagnosed gout and hyperuricemia and their differences before and after adjusting for potential socioclinical risk factors. <h3>Results</h3> A total of 18 693 participants were included in the analysis, consisting of 3304 Black women (mean [SD] age, 44.8 [0.4] years), 6195 White women (mean [SD] age, 49.8 [0.3] years), 3085 Black men (mean [SD] age, 43.6 [0.5] years]), and 6109 White men (mean [SD] age, 48.2 [0.3] years). Age-standardized prevalence of gout was 3.5% (95% CI, 2.7%-4.3%) in Black women and 2.0% (95% CI, 1.5%-2.5%) in White women (age-adjusted odds ratio [OR], 1.81 [95% CI, 1.29-2.53]); prevalence was 7.0% (95% CI, 6.2%-7.9%) in Black men and 5.4% (95% CI, 4.7%-6.2%) in White men (age-adjusted OR, 1.26 [95% CI, 1.02-1.55]). These associations attenuated after adjusting for poverty, diet, body mass index, and CKD among women and for diet and CKD among men but became null after adjusting for all risk factors (ORs, 1.05 [95% CI, 0.67-1.65] among women and 1.05 [95% CI, 0.80-1.35] among men). Hyperuricemia end point findings were similar. <h3>Conclusions and Relevance</h3> In this nationally representative race- and sex-specific cross-sectional study of US adults, gout was more prevalent in adults self-reporting Black race during a recent 10-year period compared with their White counterparts. These racial differences may be explained by sex-specific differences in diet and social determinants of health and clinical factors. Culturally informed efforts focusing on these factors could reduce current gout-related disparities.
Clinical and Genetic Risk Factors for Acute Incident Venous Thromboembolism in Ambulatory Patients With COVID-19
Authors: JunQing Xie, Albert Prats-Uribe, Qi Feng, YunHe Wang, Dipender Gill, Roger Paredes, Dani Prieto-Alhambra
Journal: JAMA Internal Medicine (2022)

The risk of venous thromboembolism (VTE) in ambulatory COVID-19 is controversial. In addition, the association of vaccination with COVID-19-related VTE and relevant clinical and genetic risk factors remain to be elucidated.To quantify the association between ambulatory COVID-19 and short-term risk of VTE, study the potential protective role of vaccination, and investigate clinical and genetic risk factors for post-COVID-19 VTE.This population-based cohort study of patients with COVID-19 from UK Biobank included participants with SARS-CoV-2 infection that was confirmed by a positive polymerase chain test reaction result between March 1, 2020, and September 3, 2021, who were then propensity score matched to COVID-19-naive people during the same period. Participants with a history of VTE who used antithrombotic drugs (1 year before index dates) or tested positive in hospital were excluded.First infection with SARS-CoV-2, age, sex, ethnicity, socioeconomic status, obesity, vaccination status, and inherited thrombophilia.The primary outcome was a composite VTE, including deep vein thrombosis or pulmonary embolism, which occurred 30 days after the infection. Hazard ratios (HRs) with 95% CIs were calculated using cause-specific Cox models.In 18 818 outpatients with COVID-19 (10 580 women [56.2%]; mean [SD] age, 64.3 [8.0] years) and 93 179 matched uninfected participants (52 177 women [56.0%]; mean [SD] age, 64.3 [7.9] years), the infection was associated with an increased risk of VTE in 30 days (incidence rate of 50.99 and 2.37 per 1000 person-years for infected and uninfected people, respectively; HR, 21.42; 95% CI, 12.63-36.31). However, risk was substantially attenuated among the fully vaccinated (HR, 5.95; 95% CI, 1.82-19.5; interaction P = .02). In patients with COVID-19, older age, male sex, and obesity were independently associated with higher risk, with adjusted HRs of 1.87 (95% CI, 1.50-2.33) per 10 years, 1.69 (95% CI, 1.30-2.19), and 1.83 (95% CI, 1.28-2.61), respectively. Further, inherited thrombophilia was associated with an HR of 2.05 (95% CI, 1.15-3.66) for post-COVID-19 VTE.In this population-based cohort study of patients with COVID-19, ambulatory COVID-19 was associated with a substantially increased risk of incident VTE, but this risk was greatly reduced in fully vaccinated people with breakthrough infection. Older age, male sex, and obesity were clinical risk factors for post-COVID-19 VTE; factor V Leiden thrombophilia was additionally associated with double the risk, comparable with the risk of 10-year aging. These findings may reinforce the need for vaccination, inform VTE risk stratification, and call for targeted VTE prophylaxis strategies for unvaccinated outpatients with COVID-19.
Patterns of Practice and Improvements in Survival Among Patients With Stage 2/3 Rectal Cancer Treated With Trimodality Therapy
Authors: Hagen F. Kennecke, Henry T. Bahnson, Bruce Lin, Colin O’Rourke, Jennifer Kaplan, Huong Pham, Andrew Suen, Vlad V. Simianu
Journal: JAMA Oncology (2022)

This study quantifies the trends in trimodality therapy use and its association with pathologic stage and overall survival of patients with rectal cancer at the population level.To describe changes between 2006 and 2016 in the sequence and use of chemotherapy/radiation therapy (C/RT), multiagent (MA) chemotherapy, and total neoadjuvant therapy (TNT) for patients with stage 2/3 rectal cancer and identify associations with pathologic stage and survival over time.This retrospective cohort analysis included patient records from the National Cancer Database between 2006 and 2016. Of 110 372 patient records, 77 905 were excluded owing to not receiving trimodality therapy and other predefined exclusion criteria. The final analytic cohort comprised 32 467 patients records treated with trimodality therapy, with 24 297 considered in the survival analysis. Data analysis was performed between June 2020 and December 2021.Trimodality therapy was defined as including all of the following: definitive surgery; radiation therapy (RT), alone or in combination with chemotherapy; and neoadjuvant/adjuvant single-agent (SA) or multiagent (MA) chemotherapy independent of RT.Using Cox multivariable survival analyses across demographics, surgery type, stage, year of diagnosis, and facility type, treatment groups were allocated as the following: group A: TNT (n = 8883 [27%]); group B: preoperative C/RT plus postoperative SA chemotherapy (n = 5967 [18%]); group C: preoperative C/RT plus postoperative MA chemotherapy (n = 12 926 [40%]); and group D: postoperative C/RT plus MA chemotherapy (n = 4689 [14%]).The final analytic cohort comprised 32 467 patients (mean [SD] age at diagnosis, 57.6 [11.6] years; 12 549 [38.7%] women and 19 918 [61.3%] men). Comparing 2016 with 2006, treatment shifted to fewer patients receiving postoperative C/RT (group D) (28% vs 8%; P < .001), and more preoperative C/RT and postoperative MA chemotherapy (group C) (24% vs 45%; P < .001) being used. While clinical stage 2 and 3 distribution remained unchanged, pathologic downstaging was observed to stages 0, 1, 2, and 3: 0.60%, 10%, 31%, and 57% vs 2.8%, 22%, 29%, and 45%, from 2006 to 2015, respectively (P < .001). More recent year of diagnosis was associated with an adjusted hazard ratio of 0.77 (95% CI, 0.67-0.87) for mortality within 36 months after diagnosis (2015 vs 2006).In this cohort study, the shift toward preoperative C/RT and lower pathologic stage was associated with improved overall survival in stage 2/3 rectal cancers.
A Phase I Trial of CT900, a Novel α-Folate Receptor–Mediated Thymidylate Synthase Inhibitor, in Patients with Solid Tumors with Expansion Cohorts in Patients with High-Grade Serous Ovarian Cancer
Authors: Susana Banerjee, Vasiliki Michalarea, Joo Ern Ang, Alvaro Ingles Garces, Andrea Biondo, Ionut-Gabriel Funingana, Martin Little, Ruth Ruddle, Florence Raynaud, Ruth Riisnaes, Bora Gurel, Sue Chua, Nina Tunariu, Joanna C. Porter, Toby Prout, Mona Parmar, Anna Zachariou, Alison Turner, Ben Jenkins, Stuart McIntosh, Ed Ainscow, Anna Minchom, Juanita Lopez, Johann de Bono, Robert Jones, Emma Hall, Natalie Cook, Bristi Basu, Udai Banerji
Journal: Clinical Cancer Research (2022)

Abstract Purpose: CT900 is a novel small molecule thymidylate synthase inhibitor that binds to α-folate receptor (α-FR) and thus is selectively taken up by α-FR–overexpressing tumors. Patients and Methods: A 3+3 dose escalation design was used. During dose escalation, CT900 doses of 1–6 mg/m2 weekly and 2–12 mg/m2 every 2 weeks (q2Wk) intravenously were evaluated. Patients with high-grade serous ovarian cancer were enrolled in the expansion cohorts. Results: 109 patients were enrolled: 42 patients in the dose escalation and 67 patients in the expansion cohorts. At the dose/schedule of 12 mg/m2/q2Wk (with and without dexamethasone, n = 40), the most common treatment-related adverse events were fatigue, nausea, diarrhea, cough, anemia, and pneumonitis, which were predominantly grade 1 and grade 2. Levels of CT900 more than 600 nmol/L needed for growth inhibition in preclinical models were achieved for &amp;gt;65 hours at a dose of 12 mg/m2. In the expansion cohorts, the overall response rate (ORR), was 14/64 (21.9%). Thirty-eight response-evaluable patients in the expansion cohorts receiving 12 mg/m2/q2Wk had tumor evaluable for quantification of α-FR. Patients with high or medium expression had an objective response rate of 9/25 (36%) compared with 1/13 (7.7%) in patients with negative/very low or low expression of α-FR. Conclusions: The dose of 12 mg/m2/q2Wk was declared the recommended phase II dose/schedule. At this dose/schedule, CT900 exhibited an acceptable side effect profile with clinical benefit in patients with high/medium α-FR expression and warrants further investigation.
Proteomic Markers of DNA Repair and PI3K Pathway Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer
Authors: Robert J. Cardnell, Ying Feng, Lixia Diao, You-Hong Fan, Fatemah Masrorpour, Jing Wang, Yuqiao Shen, Gordon B. Mills, John D. Minna, John V. Heymach, Lauren A. Byers
Journal: Clinical Cancer Research (2013)

Abstract Purpose: Small cell lung carcinoma (SCLC) is an aggressive malignancy affecting nearly 30,000 people annually in the United States. We have previously identified elevated PARP1 levels in SCLC and demonstrated in vitro sensitivity to the PARP inhibitors AZD 2281 and AG014699. Here, we evaluate activity of a novel, potent PARP inhibitor, BMN 673, and identify markers of response as a basis for developing predictive markers for clinical application. Experimental Design: Inhibition of SCLC proliferation by BMN 673 was assayed in vitro and effects on tumor growth were measured in SCLC xenograft models. Protein expression and pathway activation was assessed by reverse phase protein array and western blot analysis. PARP inhibition was confirmed using a PAR ELISA. Results: We demonstrate striking, single agent activity of BMN 673 in SCLC cell lines and xenografts, with single agent BMN 673 exhibiting in vivo activity similar to cisplatin. Sensitivity to BMN 673 was associated with elevated baseline expression levels of several DNA repair proteins, whereas greater drug resistance was observed in SCLC models with baseline activation of the PI3K/mTOR pathway. Furthermore, we developed and confirmed these data with a novel “DNA repair score” consisting of a group of 17 DNA repair proteins. Conclusions: Elevated expression of multiple DNA repair proteins, as well as a corresponding “DNA repair protein score,” predict response to BMN 673 in in vitro SCLC models. These observations complement recent work in which PI3K inhibition sensitizes breast cancer models to PARP inhibition, suggesting cooperation between DNA repair and PI3K pathways. Clin Cancer Res; 19(22); 6322–8. ©2013 AACR.
Textbook of General Surgery.
Journal: JAMA (1952)

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Potent and Selective PTDSS1 Inhibitors Induce Collateral Lethality in Cancers with PTDSS2 Deletion
Authors: Yohei Yoshihama, Hidenori Namiki, Taiga Kato, Naomi Shimazaki, Sachiko Takaishi, Kumiko Kadoshima-Yamaoka, Hideo Yukinaga, Naoyuki Maeda, Tomoko Shibutani, Kazunori Fujimoto, Makoto Hirasawa, Hiroki Goto, Naoya Wada, Shinji Tsutsumi, Yasuhide Hirota, Tomoki Ishikawa, Shoji Yamamoto
Journal: Cancer Research (2022)

This study identifies a specific dependency on PTDSS1 for phosphatidylserine synthesis following PTDSS2 deletion and introduces novel PTDSS1 inhibitors as a therapeutic option to induce collateral lethality in cancer with PTDSS2 loss.